39 research outputs found
iHMS: a database integrating human histone modification data across developmental stages and tissues
No full textYanglan Gan1,†, Han Tao2,†, Jihong Guan2,* and Shuigeng Zhou3,*
1 School of Computer Science and Technology, Donghua
University, Shanghai 201620, China,2Department
of Computer Science and Technology, Tongji University, Shanghai 201804, China,3Shanghai Key Lab of Intelligent Information Processing, and School
of Computer Science, Fudan University,Shanghai200433, China.
*Corresponding authors: Tel:86-21-65654504;
Email: [email protected]; [email protected]
†The authors
contribute equally to the work.</p
Effects of Lanthanum Modified Bentonite and Polyaluminium Chloride on the Environmental Variables in the Water and Sediment Phosphorus Form in Lake Yanglan, China
No full textThe application of lanthanum modified bentonite (Phoslock®) and polyaluminium chloride (PAC) is popular in the restoration of European temperate lakes; however, the effects of the application on the concentrations of phosphorus (P) in both the water and the sediments have been poorly evaluated to date. We studied the effects of the application of Phoslock® + PAC on the concentrations of total phosphorus (TP), particulate phosphorus (PP), soluble reactive phosphorus (SRP), total suspended solids (TSS) and chlorophyll a (Chla) in the water, and different P forms in the sediments, in an isolated part of Lake Yanglan. The results showed that the concentrations of TP, PP, SRP, TSS and Chla decreased significantly after the addition of Phoslock® + PAC. Moreover, the concentrations of labile-P, reductant-soluble-P and organic-P in the sediments were also significantly decreased after the Phoslock® + PAC application. However, the concentrations of both the stable apatite-P and residual-P in the sediments after application of Phoslock® + PAC were much higher than the pre-addition values, while the concentrations of metal-oxide-P did not differ significantly between the pre- and post- application conditions. Our findings imply that the combined application of Phoslock® and PAC can be used in the restoration of subtropical shallow lakes, to reduce the concentrations of P in the water and suppress the release of P from the sediments
iHHMD: a database integrating human histone modification data across developmental stag-es and tissues
No full text<p>This is the way we proprocess in our database</p
iHMS
No full textiHMS: a database integrating human histone modification data across developmental stages and tissue
Historical Origin & Social Transformation of the Hui Nationality of Hainan Province : A Historical & Anthropological Study of Two Hui Nationality Villages of Yanglan Town, Sanya City
No full text中国の南端にある海南島三亜市羊欄鎮回輝村，回新村は，海南省内で唯一の
回族集居地である。2002 年には，1218 戸，6,400 人の回族人口を有していた。
1983 年12 月から2003 年3 月までの間に，筆者は合計8 回にわたって回輝，回
新両村でのフィールドワークを行った。本稿は，このフィールドワーク資料を
基に，歴史学，人類学，考古学，言語学の関連資料をも参照しながら，海南回
族の歴史来源および羊欄回族コミュニティーの社会変化の過程について論じよ
うとするものである。
海南島の回族には，2 つの主要な来源がある。一つは唐宋時代に中国に来住
したアラビア人商人であり，もう一つは宋元二代に占城（チャンパ）から移住
してきたイスラム教徒である。
唐宋時代には，イスラム教を信仰するアラビア人商人が，「海上のシルク
ロード」沿いに広州，泉州など中国の沿海都市に来住し，貿易活動に従事し
た。海南島はアラビア商船の通り道であった。それらアラビア人商人の一部分
は，台風や海賊の被害によって，海南島東南部の陵水，万寧，崖県（現在の三
亜市）など沿海地区に居留することになった。
明末清初から1943 年までの間は，三亜里という地点が羊欄回族の唯一の集
居地であった。1943 年には，日本軍がこの地点に飛行場を建設したために，当
地の回族は現在の回輝村に移転させられた。1945 年の終戦の後，回族の一部は
もとの村に戻り，地名を回新と改め，こうして現在の回輝・回新両村落からな
る回族コミュニティーができあがった。
羊欄の回族社会では，1980 年代になって経済，文化等の方面で非常に大きな
変化が生じた。80 年代後半には，三亜市の発展にともなってコミュニティー全
体に衆人の注目を集める一大変化が生じたが，その主要なものは以下の四方面
の変化である。
1．産業構造の変革
回輝，回新両村は海辺に位置していたので，回族の人々は代々魚を捕るこ
とを主要な生活手段としてきた。漁船は小型で性能の低いものだったので，沖
合い漁業には適さず，収入は少なかったので，回族の人々の生活は極めて貧し
かった。1987 年の両村住民の平均年収は200 元強であり，羊欄鎮の中でも最も
低収入の村であった。
1987 年に三亜が県レベルから地区レベルの市に昇格した後，省政府は「三亜
を現代的国際ビーチリゾート都市に」という全体目標を掲げ，これによって不
動産開発ブームと観光産業の隆盛が引き起こされた。羊欄の回族はこの機を捉
え，一連の経済活動に取り組み，わずか十数年のうちには運送業，観光販売・
サービス業，青果の卸し・小売業を筆頭に，多様な経営活動を含む新たな経済
発展の局面が到来して，この村は鎮の中でも最も裕福な村へと変身したのであ
る。
2．生活様式の変化
経済的収入の増加は，生活様式の変化を生み出した。まず，住居の様態が変
わり，低層の草葺き屋根はスレート葺き家屋やビルになった。また，交通手段
が改善され，徒歩や自転車に代わってモータリゼーションが生じた。さらに，
生活用品が多様化，高級化した。
3．価値観および行動パターンの革新
1980 年代以前には，回族コミュニティーの住民は，中国農村一般と同じく
「靠山吃山，靠海吃海」（山にあれば山の幸を食べ，海にあれば海の幸を食べ
る）の伝統的な自然経済観念を墨守していた。80 年代に中国が改革開放を実行
して以降，回族の人々は「法律・道徳に触れない限り，金の稼げることならな
んでもする」という価値観をもつようになった。そして，回族コミュニティー
の経済状況は，量的変化と，質的飛躍を成し遂げたのである。
伝統的観念と，行動パターンの変化にともない，羊欄の回族女性は，家庭の
外に出て各種の経済活動に携わるようになり，家計の担い手の主力となった。
4．伝統文化の継承と発揚
回族は，イスラム教を信仰する民族であり，回族の伝統文化は，至る部分に
おいて，イスラム文化の刻印を受けている。伝統文化の継承と発揚のため，羊
欄の回族は以下のいくつかの措置を採用している。
まず，モスクの再建・新設を，伝統文化の発揚上の最重要事項とし，1990 年
代には，6 個のモスクが次々と再建・新設された。
また，地元での宗教的人材の養成を重視し，80 年代以来，十数名の優秀な青
年を，サウジアラビア，イランなどの国家のイスラム学校へ留学させ，帰国後
は各モスクで，教長や，アホンを担当したり，宗教教育活動に従事したりして
いる。
さらに，青少年に対する宗教文化知識の普及に努め，各モスクではコーラン
学校を開いている。
そして，宗教生活並びに日常生活上，イスラム教の教義としきたりを遵守し
ている。Huihui Village and Huixin Village, located in Yanglan Town, Sanya City,
Hainan Island in south China, are the two only compact communities of Hui
Nationality in Hainan Province. In 2002, there were 1218 households of Hui
Nationality and 6400 Hui people lived there. From December 1983 to March
2003, the author visited these two villages 8 times in succession to do field
research. In this article, the author will try to analyze the historical origin of
the Hui Nationality of Hainan Province and the social transformation of the
Hui community of Yanglan Town based on material obtained through fieldwork
and other data of history, anthropology, archaeology and linguistics.
There are two main origins of the Hui Nationality of Hainan. One consisted
of Arabian merchants who came to China during the Tang and Song
Dynasties. The other consisted of Muslims who immigrated from Zhancheng
in Vietnam during the Song and Yuan Dynasties.
During the Tang and Song Dynasties, many Muslim Arabian merchants
came to Guangzhou, Quanzhou and other coastal cities of China along “the
Silk Road on the Sea” to do business. Hainan was then an important destination
for Arabian merchant vessels. During these times, some of those Arabian
merchants were forced to stay in Lingshui, Wanning, Ya County (now named
Sanya City) and some other coastal regions in the south-east part of Hainan
due to typhoons or the attacks of pirates. As time went by, most of the offspring
of these Arabian businessmen were assimilated into the local Han, Li
and Miao Nationalities. Some other descendants developed into the ancestors
of the Hui Nationality of Yanglan Town.
During the Song and Yuan Dynasties, many Muslims from Zhancheng,
Vietnam immigrated into Dan County, Ya County, Wanning and some other
coastal areas of Hainan in order to avoid the turmoils of typhoons and wars.
The majority of those Muslims living in Dan County and Wanning are assimilated
into other local nationalities. The offspring of the Muslims dwelling
mainly in Ya County moved to Suosanya Li (now the site of Huixin Village,
Yanglan Town, Sanya City) of Ya County about the end of the Ming Dynasty
and the beginning of the Qing Dynasty. They formed a Hui community with a
collective dwelling place, joint economic livelihood, a common language and
customs there.
Between the end of the Ming Dynasty and the beginning of the Qing
Dynasty, Suosanya Li was the only compact community of Hui Nationality in
Yanglan Town. In 1943, they were forced to move to Huihui Village because
the Japanese army planned to construct an airport there. When the war ended
in 1945, some of them moved back and named it “Huixin”, and thus these
two compact communities of Hui Nationality came into being.
The economy and culture of these communities saw no great changes
from the time they settled there to the beginning of the 1980s. But in the late
1980s, the whole community changed greatly along with the urbanization of
Sanya City as follows:
1. Reformation of industrial structure
Huihui Village and Huixin Village are both located on the seacoast. Fishing
was the traditional means to make a living for generations. Because the
boats were small, poorly constructed and not suitable for deep sea fishing, the
people couldn’t earn enough to make ends meet and they lived a very miserable
life. In 1987, the average annual income per person in these two villages
was RMB200 or so, the lowest in Yanglan Town.
After Sanya was elevated from a city of county level to a city of prefecture
level in 1987, the Hainan Provincial government put forward the overall
goal of “transforming Sanya into a modernized international seacoast tourist
city”. This brought about a tide of development of real estate and a blooming
of the local tourist industry. The Hui people of Yanglan took advantage of
this great opportunity to carry out a range of economic activities during this
period. Just in a few years, they formed a new economic pattern with such
leading industries as traffic services, tourism, trade and the whole & retail
sale of fruit and vegetables. Now these two villages are the richest in Yanglan
Town.
2. Transformation of life styles
The increase of income caused the transformation of life styles.
Change of living environment: Low thatched cottages have been replaced
by tile-roofed houses and multi-storied buildings.
Improvement of traffic conditions: Motor vehicles have been used widely
to substitute for walking or cycling.
Diversification and improvement in quality of daily necessities.
3. Innovation in values and behavioral orientation.
Before the 1980s, the members of the Hui Communities cherished the
traditional values of the natural economy: “those living on a mountain live
off the mountain, those living near the water live off the water”, just like the
inhabitants of other Chinese rural areas. After the “Reformation and Opening
to the World” of China in the 1980s, the members of the Hui Nationality
began to uphold the different value “every profession is good as long as it can
produce a profit and won’t violate the law and discipline.” The transformation
of their values did much to help in the improvement of the local economy and
society.
Along with the innovation in values and behavioral orientation, the
women of Hui Nationality of Yanglan began to leave the home and take part
in all sorts of economic activities and are now the main leaders in making
fortunes.
4. Continuation and development of traditional cultures.
Hui is a Muslim nationality. The traditional cultures of the Hui Nationality
are all deeply influenced by Muslim cultures. In order to carry forward
and develop traditional cultures, the Hui people of Yanglan took certain measures
as follows:
The construction and reconstruction of mosques is a matter of prime
importance in spreading and developing traditional cultures. About 6 mosques
were constructed or reconstructed in the 1990s.
Training local religious professionals. More than 10 outstanding youths
were sent abroad to study in the Muslim schools of Saudi Arabia, Iran and
some other countries and they were appointed as deans, imams or engaged in
religious education after graduation.
Popularization of religious knowledge among the youth. Religious education
in every mosque.
Abiding by the canons and ceremonies of Islam both in religious activities
and everyday life.departmental bulletin pape
A comparison study on feature selection of DNA structural properties for promoter prediction
No full textAbstract Background Promoter prediction is an integrant step for understanding gene regulation and annotating genomes. Traditional promoter analysis is mainly based on sequence compositional features. Recently, many kinds of structural features have been employed in promoter prediction. However, considering the high-dimensionality and overfitting problems, it is unfeasible to utilize all available features for promoter prediction. Thus it is necessary to choose some appropriate features for the prediction task. Results This paper conducts an extensive comparison study on feature selection of DNA structural properties for promoter prediction. Firstly, to examine whether promoters possess some special structures, we carry out a systematical comparison among the profiles of thirteen structural features on promoter and non-promoter sequences. Secondly, we investigate the correlations between these structural features and promoter sequences. Thirdly, both filter and wrapper methods are utilized to select appropriate feature subsets from thirteen different kinds of structural features for promoter prediction, and the predictive power of the selected feature subsets is evaluated. Finally, we compare the prediction performance of the feature subsets selected in this paper with nine existing promoter prediction approaches. Conclusions Experimental results show that the structural features are differentially correlated to promoters. Specifically, DNA-bending stiffness, DNA denaturation and energy-related features are highly correlated with promoters. The predictive power for promoter sequences differentiates greatly among different structural features. Selecting the relevant features can significantly improve the accuracy of promoter prediction.</p
Structural features based genome-wide characterization and prediction of nucleosome organization
No full textAbstract Background Nucleosome distribution along chromatin dictates genomic DNA accessibility and thus profoundly influences gene expression. However, the underlying mechanism of nucleosome formation remains elusive. Here, taking a structural perspective, we systematically explored nucleosome formation potential of genomic sequences and the effect on chromatin organization and gene expression in S. cerevisiae. Results We analyzed twelve structural features related to flexibility, curvature and energy of DNA sequences. The results showed that some structural features such as DNA denaturation, DNA-bending stiffness, Stacking energy, Z-DNA, Propeller twist and free energy, were highly correlated with in vitro and in vivo nucleosome occupancy. Specifically, they can be classified into two classes, one positively and the other negatively correlated with nucleosome occupancy. These two kinds of structural features facilitated nucleosome binding in centromere regions and repressed nucleosome formation in the promoter regions of protein-coding genes to mediate transcriptional regulation. Based on these analyses, we integrated all twelve structural features in a model to predict more accurately nucleosome occupancy in vivo than the existing methods that mainly depend on sequence compositional features. Furthermore, we developed a novel approach, named DLaNe, that located nucleosomes by detecting peaks of structural profiles, and built a meta predictor to integrate information from different structural features. As a comparison, we also constructed a hidden Markov model (HMM) to locate nucleosomes based on the profiles of these structural features. The result showed that the meta DLaNe and HMM-based method performed better than the existing methods, demonstrating the power of these structural features in predicting nucleosome positions. Conclusions Our analysis revealed that DNA structures significantly contribute to nucleosome organization and influence chromatin structure and gene expression regulation. The results indicated that our proposed methods are effective in predicting nucleosome occupancy and positions and that these structural features are highly predictive of nucleosome organization. The implementation of our DLaNe method based on structural features is available online.</p
A new method for enhancer prediction based on deep belief network
No full textAbstract Background Studies have shown that enhancers are significant regulatory elements to play crucial roles in gene expression regulation. Since enhancers are unrelated to the orientation and distance to their target genes, it is a challenging mission for scholars and researchers to accurately predicting distal enhancers. In the past years, with the high-throughout ChiP-seq technologies development, several computational techniques emerge to predict enhancers using epigenetic or genomic features. Nevertheless, the inconsistency of computational models across different cell-lines and the unsatisfactory prediction performance call for further research in this area. Results Here, we propose a new Deep Belief Network (DBN) based computational method for enhancer prediction, which is called EnhancerDBN. This method combines diverse features, composed of DNA sequence compositional features, DNA methylation and histone modifications. Our computational results indicate that 1) EnhancerDBN outperforms 13 existing methods in prediction, and 2) GC content and DNA methylation can serve as relevant features for enhancer prediction. Conclusion Deep learning is effective in boosting the performance of enhancer prediction
